.TH g_gyrate 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_gyrate - calculates the radius of gyration

.B VERSION 4.5
.SH SYNOPSIS
\f3g_gyrate\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-o" " gyrate.xvg "
.BI "\-acf" " moi\-acf.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-nmol" " int "
.BI "\-[no]q" ""
.BI "\-[no]p" ""
.BI "\-[no]moi" ""
.BI "\-nz" " int "
.BI "\-acflen" " int "
.BI "\-[no]normalize" ""
.BI "\-P" " enum "
.BI "\-fitfn" " enum "
.BI "\-ncskip" " int "
.BI "\-beginfit" " real "
.BI "\-endfit" " real "
.SH DESCRIPTION
\&g_gyrate computes the radius of gyration of a group of atoms
\&and the radii of gyration about the x, y and z axes,
\&as a function of time. The atoms are explicitly mass weighted.


\&With the \fB \-nmol\fR option the radius of gyration will be calculated
\&for multiple molecules by splitting the analysis group in equally
\&sized parts.


\&With the option \fB \-nz\fR 2D radii of gyration in the x\-y plane
\&of slices along the z\-axis are calculated.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " gyrate.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-acf" " moi\-acf.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-nmol"  " int" " 1" 
 The number of molecules to analyze

.BI "\-[no]q"  "no    "
 Use absolute value of the charge of an atom as weighting factor instead of mass

.BI "\-[no]p"  "no    "
 Calculate the radii of gyration about the principal axes.

.BI "\-[no]moi"  "no    "
 Calculate the moments of inertia (defined by the principal axes).

.BI "\-nz"  " int" " 0" 
 Calculate the 2D radii of gyration of  slices along the z\-axis

.BI "\-acflen"  " int" " \-1" 
 Length of the ACF, default is half the number of frames

.BI "\-[no]normalize"  "yes   "
 Normalize ACF

.BI "\-P"  " enum" " 0" 
 Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR

.BI "\-fitfn"  " enum" " none" 
 Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR

.BI "\-ncskip"  " int" " 0" 
 Skip N points in the output file of correlation functions

.BI "\-beginfit"  " real" " 0     " 
 Time where to begin the exponential fit of the correlation function

.BI "\-endfit"  " real" " \-1    " 
 Time where to end the exponential fit of the correlation function, \-1 is until the end

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
